Multiple sequence alignment - TraesCS7B01G211600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G211600 chr7B 100.000 5078 0 0 1 5078 387164850 387159773 0.000000e+00 9378
1 TraesCS7B01G211600 chr7B 85.685 496 62 7 1 490 611040474 611040966 9.750000e-142 514
2 TraesCS7B01G211600 chr7B 93.220 118 8 0 2912 3029 594029893 594030010 1.880000e-39 174
3 TraesCS7B01G211600 chr7D 95.917 2302 75 7 624 2915 390693589 390691297 0.000000e+00 3712
4 TraesCS7B01G211600 chr7D 91.934 1748 62 33 3360 5077 390690896 390689198 0.000000e+00 2374
5 TraesCS7B01G211600 chr7D 85.714 490 64 6 3 491 190088181 190087697 3.510000e-141 512
6 TraesCS7B01G211600 chr7D 94.921 315 10 4 3046 3356 390691257 390690945 5.910000e-134 488
7 TraesCS7B01G211600 chr7A 94.971 1750 51 15 3360 5077 442272960 442271216 0.000000e+00 2710
8 TraesCS7B01G211600 chr7A 94.502 1637 50 19 571 2205 442275571 442273973 0.000000e+00 2488
9 TraesCS7B01G211600 chr7A 91.954 609 30 5 2198 2805 442273596 442273006 0.000000e+00 835
10 TraesCS7B01G211600 chr4B 77.837 1322 178 41 807 2114 40074178 40075398 0.000000e+00 712
11 TraesCS7B01G211600 chr5D 87.221 493 59 4 1 492 458530643 458530154 4.440000e-155 558
12 TraesCS7B01G211600 chr3B 86.613 493 60 5 1 490 404416590 404417079 1.610000e-149 540
13 TraesCS7B01G211600 chr2D 85.300 517 67 8 15 527 651313995 651314506 4.500000e-145 525
14 TraesCS7B01G211600 chr1D 85.801 493 66 3 1 491 250734486 250734976 2.100000e-143 520
15 TraesCS7B01G211600 chr1D 86.498 474 59 5 1 473 58564406 58563937 2.710000e-142 516
16 TraesCS7B01G211600 chr6D 85.772 499 58 9 1 491 437927086 437926593 2.710000e-142 516
17 TraesCS7B01G211600 chr6D 85.510 490 67 4 3 490 104573263 104573750 4.540000e-140 508
18 TraesCS7B01G211600 chr4D 77.851 912 129 23 887 1787 27395046 27395895 9.820000e-137 497
19 TraesCS7B01G211600 chr4D 87.037 324 39 3 1791 2113 27395870 27396191 3.740000e-96 363
20 TraesCS7B01G211600 chr6A 94.318 264 15 0 2652 2915 498097133 498097396 6.120000e-109 405
21 TraesCS7B01G211600 chr6A 89.297 327 23 9 3046 3362 498097433 498097757 2.850000e-107 399
22 TraesCS7B01G211600 chr6A 92.742 124 9 0 2908 3031 612908 612785 4.040000e-41 180
23 TraesCS7B01G211600 chr6A 93.805 113 7 0 3360 3472 498097792 498097904 2.430000e-38 171
24 TraesCS7B01G211600 chr4A 88.308 325 35 3 1791 2114 575780651 575780329 2.220000e-103 387
25 TraesCS7B01G211600 chr4A 80.256 390 54 8 1399 1787 575780993 575780626 6.480000e-69 272
26 TraesCS7B01G211600 chr5B 94.872 117 6 0 2914 3030 69911041 69910925 3.120000e-42 183
27 TraesCS7B01G211600 chr5B 92.500 120 9 0 2911 3030 636599123 636599242 6.760000e-39 172
28 TraesCS7B01G211600 chr6B 92.683 123 9 0 2907 3029 77108989 77108867 1.450000e-40 178
29 TraesCS7B01G211600 chr6B 93.333 120 7 1 2914 3033 102180009 102179891 5.230000e-40 176
30 TraesCS7B01G211600 chr6B 93.333 120 7 1 2914 3032 656170558 656170439 5.230000e-40 176
31 TraesCS7B01G211600 chr1B 93.966 116 7 0 2914 3029 643050287 643050172 5.230000e-40 176
32 TraesCS7B01G211600 chr1A 93.162 117 8 0 2913 3029 425722526 425722410 6.760000e-39 172


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G211600 chr7B 387159773 387164850 5077 True 9378.000000 9378 100.000000 1 5078 1 chr7B.!!$R1 5077
1 TraesCS7B01G211600 chr7D 390689198 390693589 4391 True 2191.333333 3712 94.257333 624 5077 3 chr7D.!!$R2 4453
2 TraesCS7B01G211600 chr7A 442271216 442275571 4355 True 2011.000000 2710 93.809000 571 5077 3 chr7A.!!$R1 4506
3 TraesCS7B01G211600 chr4B 40074178 40075398 1220 False 712.000000 712 77.837000 807 2114 1 chr4B.!!$F1 1307
4 TraesCS7B01G211600 chr2D 651313995 651314506 511 False 525.000000 525 85.300000 15 527 1 chr2D.!!$F1 512
5 TraesCS7B01G211600 chr4D 27395046 27396191 1145 False 430.000000 497 82.444000 887 2113 2 chr4D.!!$F1 1226
6 TraesCS7B01G211600 chr6A 498097133 498097904 771 False 325.000000 405 92.473333 2652 3472 3 chr6A.!!$F1 820
7 TraesCS7B01G211600 chr4A 575780329 575780993 664 True 329.500000 387 84.282000 1399 2114 2 chr4A.!!$R1 715

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
920 931 0.104671 GTCCTGCTCTGCCATCTCTC 59.895 60.0 0.0 0.0 0.00 3.20 F
1103 1114 0.896940 GCAATGGGGATGATGCCGAT 60.897 55.0 0.0 0.0 32.73 4.18 F
2929 3367 0.251297 TGTTACTCCCTCCGTCCGAA 60.251 55.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2911 3349 0.890683 TTTCGGACGGAGGGAGTAAC 59.109 55.0 0.0 0.0 0.00 2.50 R
3011 3449 0.702902 AGTACTCCCTCCGTCTGGAA 59.297 55.0 0.0 0.0 45.87 3.53 R
4377 4908 0.110192 GCGCAAGGAACCGAAAAGAG 60.110 55.0 0.3 0.0 38.28 2.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.158914 TGGTTCACGCTAGCATGATGAT 60.159 45.455 15.13 0.00 0.00 2.45
33 34 1.885359 GCTAGCATGATGATGGGGGTG 60.885 57.143 10.63 0.00 0.00 4.61
39 40 1.911454 TGATGATGGGGGTGGAGATT 58.089 50.000 0.00 0.00 0.00 2.40
49 50 2.158608 GGGGTGGAGATTATGAAGGTGG 60.159 54.545 0.00 0.00 0.00 4.61
60 61 2.455674 TGAAGGTGGATCTCAACACG 57.544 50.000 0.00 0.00 38.46 4.49
79 80 0.680061 GGTGTCGTCAAGGAAGAGGT 59.320 55.000 0.00 0.00 0.00 3.85
81 82 1.340248 GTGTCGTCAAGGAAGAGGTCA 59.660 52.381 0.00 0.00 0.00 4.02
101 102 0.391661 TGGTTCGAGAAGATGCAGGC 60.392 55.000 0.00 0.00 0.00 4.85
108 109 0.463295 AGAAGATGCAGGCCGACATG 60.463 55.000 17.07 1.62 0.00 3.21
122 123 0.716108 GACATGCTCAAGTTCGACGG 59.284 55.000 0.00 0.00 0.00 4.79
136 137 0.586802 CGACGGCGAGTGATCTATGA 59.413 55.000 16.62 0.00 40.82 2.15
137 138 1.197949 CGACGGCGAGTGATCTATGAT 59.802 52.381 16.62 0.00 40.82 2.45
138 139 2.590073 GACGGCGAGTGATCTATGATG 58.410 52.381 16.62 0.00 0.00 3.07
141 142 1.344458 GCGAGTGATCTATGATGGCG 58.656 55.000 0.00 0.00 0.00 5.69
144 145 2.227626 CGAGTGATCTATGATGGCGAGT 59.772 50.000 0.00 0.00 0.00 4.18
147 148 1.966354 TGATCTATGATGGCGAGTGCT 59.034 47.619 0.00 0.00 42.25 4.40
157 158 1.730064 TGGCGAGTGCTATCGTTTTTC 59.270 47.619 11.76 0.00 44.53 2.29
166 167 2.536803 GCTATCGTTTTTCGTATGCCGA 59.463 45.455 0.00 0.00 45.66 5.54
175 176 0.599060 TCGTATGCCGACAAGTGTGA 59.401 50.000 0.00 0.00 41.60 3.58
219 220 1.521681 CGATCAAACTCCCGCCCTC 60.522 63.158 0.00 0.00 0.00 4.30
232 233 0.318107 CGCCCTCTTTTTGTGTGCTG 60.318 55.000 0.00 0.00 0.00 4.41
242 243 1.036481 TTGTGTGCTGGCATGTGTGT 61.036 50.000 0.00 0.00 0.00 3.72
246 247 2.669569 GCTGGCATGTGTGTCGGT 60.670 61.111 0.00 0.00 38.61 4.69
253 254 4.961511 TGTGTGTCGGTCGCTGGC 62.962 66.667 0.00 0.00 0.00 4.85
279 280 1.174712 GCCAGCATGAACTGTGTGGT 61.175 55.000 0.00 0.00 39.69 4.16
309 311 2.846193 AGTTGACGTTGTATGTTGGCT 58.154 42.857 0.00 0.00 0.00 4.75
335 338 0.899717 ATGGTGCCGGCATGAACTTT 60.900 50.000 35.23 10.72 0.00 2.66
341 344 3.680156 GGCATGAACTTTGGGCGA 58.320 55.556 0.00 0.00 0.00 5.54
344 347 1.501741 CATGAACTTTGGGCGACGG 59.498 57.895 0.00 0.00 0.00 4.79
345 348 1.674322 ATGAACTTTGGGCGACGGG 60.674 57.895 0.00 0.00 0.00 5.28
373 376 4.384599 GCATGATCTATGGCCGCA 57.615 55.556 0.00 0.00 37.26 5.69
393 396 3.548616 GCAGGCCTTTTTCAAATTTGTGC 60.549 43.478 17.47 12.38 0.00 4.57
394 397 3.626670 CAGGCCTTTTTCAAATTTGTGCA 59.373 39.130 17.47 1.16 0.00 4.57
395 398 4.276431 CAGGCCTTTTTCAAATTTGTGCAT 59.724 37.500 17.47 7.31 0.00 3.96
397 400 4.538917 GCCTTTTTCAAATTTGTGCATGG 58.461 39.130 17.47 15.16 0.00 3.66
399 402 5.048573 GCCTTTTTCAAATTTGTGCATGGAT 60.049 36.000 17.47 0.00 0.00 3.41
415 418 2.754472 TGGATATGAAATGAGTCGCGG 58.246 47.619 6.13 0.00 0.00 6.46
416 419 2.069273 GGATATGAAATGAGTCGCGGG 58.931 52.381 6.13 0.00 0.00 6.13
417 420 2.548067 GGATATGAAATGAGTCGCGGGT 60.548 50.000 6.13 0.00 0.00 5.28
423 426 2.107041 AATGAGTCGCGGGTGTTGGA 62.107 55.000 6.13 0.00 0.00 3.53
425 428 3.509137 GAGTCGCGGGTGTTGGACA 62.509 63.158 6.13 0.00 31.93 4.02
492 495 3.341857 CGATCCAAACGGACAAAAACA 57.658 42.857 0.00 0.00 34.62 2.83
493 496 3.896122 CGATCCAAACGGACAAAAACAT 58.104 40.909 0.00 0.00 34.62 2.71
494 497 3.911964 CGATCCAAACGGACAAAAACATC 59.088 43.478 0.00 0.00 34.62 3.06
498 501 3.040099 CAAACGGACAAAAACATCGTCC 58.960 45.455 0.00 0.00 44.79 4.79
505 508 4.261825 GGACAAAAACATCGTCCATTTGGA 60.262 41.667 2.98 0.00 46.98 3.53
516 519 3.186702 TCCATTTGGATCGATGCGTTA 57.813 42.857 12.54 0.28 39.78 3.18
527 530 2.094700 TCGATGCGTTAGAGTTGCTCTT 60.095 45.455 3.87 0.00 41.50 2.85
528 531 3.128068 TCGATGCGTTAGAGTTGCTCTTA 59.872 43.478 3.87 0.00 41.50 2.10
529 532 4.045104 CGATGCGTTAGAGTTGCTCTTAT 58.955 43.478 3.87 0.00 41.50 1.73
530 533 5.008316 TCGATGCGTTAGAGTTGCTCTTATA 59.992 40.000 3.87 0.00 41.50 0.98
531 534 5.859114 CGATGCGTTAGAGTTGCTCTTATAT 59.141 40.000 3.87 0.00 41.50 0.86
532 535 7.021790 CGATGCGTTAGAGTTGCTCTTATATA 58.978 38.462 3.87 0.00 41.50 0.86
533 536 7.537649 CGATGCGTTAGAGTTGCTCTTATATAA 59.462 37.037 3.87 0.00 41.50 0.98
534 537 9.193133 GATGCGTTAGAGTTGCTCTTATATAAA 57.807 33.333 3.87 0.00 41.50 1.40
535 538 8.575565 TGCGTTAGAGTTGCTCTTATATAAAG 57.424 34.615 3.87 0.00 41.50 1.85
536 539 7.652105 TGCGTTAGAGTTGCTCTTATATAAAGG 59.348 37.037 3.87 0.00 41.50 3.11
537 540 7.866393 GCGTTAGAGTTGCTCTTATATAAAGGA 59.134 37.037 3.87 0.00 41.50 3.36
538 541 9.745880 CGTTAGAGTTGCTCTTATATAAAGGAA 57.254 33.333 3.87 2.90 41.50 3.36
542 545 8.982723 AGAGTTGCTCTTATATAAAGGAACAGA 58.017 33.333 25.36 9.67 41.95 3.41
543 546 9.601217 GAGTTGCTCTTATATAAAGGAACAGAA 57.399 33.333 25.36 5.13 41.95 3.02
544 547 9.959721 AGTTGCTCTTATATAAAGGAACAGAAA 57.040 29.630 25.36 7.25 41.95 2.52
560 563 9.700831 AGGAACAGAAAAAGTATATATTTGCCT 57.299 29.630 0.00 0.00 0.00 4.75
564 567 9.391006 ACAGAAAAAGTATATATTTGCCTTCGA 57.609 29.630 0.00 0.00 0.00 3.71
565 568 9.869844 CAGAAAAAGTATATATTTGCCTTCGAG 57.130 33.333 0.00 0.00 0.00 4.04
566 569 9.057089 AGAAAAAGTATATATTTGCCTTCGAGG 57.943 33.333 0.00 0.00 38.80 4.63
567 570 8.974060 AAAAAGTATATATTTGCCTTCGAGGA 57.026 30.769 0.00 0.00 37.67 3.71
568 571 9.574516 AAAAAGTATATATTTGCCTTCGAGGAT 57.425 29.630 0.00 0.00 37.67 3.24
569 572 8.779354 AAAGTATATATTTGCCTTCGAGGATC 57.221 34.615 0.00 0.00 37.67 3.36
583 586 6.591834 CCTTCGAGGATCAATAATACATCCAC 59.408 42.308 0.00 0.00 37.67 4.02
585 588 5.780282 TCGAGGATCAATAATACATCCACCT 59.220 40.000 0.00 0.00 38.95 4.00
601 605 3.117888 TCCACCTCATTAGCCAATCCTTC 60.118 47.826 0.00 0.00 0.00 3.46
610 614 6.560304 TCATTAGCCAATCCTTCTCTATTCCT 59.440 38.462 0.00 0.00 0.00 3.36
611 615 6.831664 TTAGCCAATCCTTCTCTATTCCTT 57.168 37.500 0.00 0.00 0.00 3.36
612 616 5.303259 AGCCAATCCTTCTCTATTCCTTC 57.697 43.478 0.00 0.00 0.00 3.46
613 617 4.974501 AGCCAATCCTTCTCTATTCCTTCT 59.025 41.667 0.00 0.00 0.00 2.85
614 618 6.146760 AGCCAATCCTTCTCTATTCCTTCTA 58.853 40.000 0.00 0.00 0.00 2.10
615 619 6.042666 AGCCAATCCTTCTCTATTCCTTCTAC 59.957 42.308 0.00 0.00 0.00 2.59
616 620 6.451393 CCAATCCTTCTCTATTCCTTCTACG 58.549 44.000 0.00 0.00 0.00 3.51
617 621 6.451393 CAATCCTTCTCTATTCCTTCTACGG 58.549 44.000 0.00 0.00 0.00 4.02
618 622 5.384145 TCCTTCTCTATTCCTTCTACGGA 57.616 43.478 0.00 0.00 0.00 4.69
619 623 5.378332 TCCTTCTCTATTCCTTCTACGGAG 58.622 45.833 0.00 0.00 33.89 4.63
620 624 4.521256 CCTTCTCTATTCCTTCTACGGAGG 59.479 50.000 0.00 0.00 33.89 4.30
621 625 4.101645 TCTCTATTCCTTCTACGGAGGG 57.898 50.000 0.00 0.00 39.72 4.30
622 626 3.158676 CTCTATTCCTTCTACGGAGGGG 58.841 54.545 0.00 0.00 38.97 4.79
631 635 3.892104 TACGGAGGGGCTTGACGGT 62.892 63.158 0.00 0.00 0.00 4.83
634 638 2.359975 GAGGGGCTTGACGGTTGG 60.360 66.667 0.00 0.00 0.00 3.77
635 639 4.660938 AGGGGCTTGACGGTTGGC 62.661 66.667 0.00 0.00 0.00 4.52
643 647 4.218478 GACGGTTGGCGCGTATGC 62.218 66.667 8.43 0.00 37.91 3.14
652 656 1.125847 GGCGCGTATGCTTTTGTTCG 61.126 55.000 8.43 0.00 39.65 3.95
662 666 1.028905 CTTTTGTTCGCTGGGTTGGA 58.971 50.000 0.00 0.00 0.00 3.53
775 779 4.706962 ACAATTTTAGAGGAGTGGGCATTC 59.293 41.667 0.00 0.00 0.00 2.67
861 866 2.079925 GATTCGCTGCCAGAAAGAACT 58.920 47.619 0.00 0.00 0.00 3.01
863 868 2.370281 TCGCTGCCAGAAAGAACTAG 57.630 50.000 0.00 0.00 0.00 2.57
920 931 0.104671 GTCCTGCTCTGCCATCTCTC 59.895 60.000 0.00 0.00 0.00 3.20
1096 1107 4.873810 CGGCGGCAATGGGGATGA 62.874 66.667 10.53 0.00 0.00 2.92
1097 1108 2.203538 GGCGGCAATGGGGATGAT 60.204 61.111 3.07 0.00 0.00 2.45
1098 1109 2.567497 GGCGGCAATGGGGATGATG 61.567 63.158 3.07 0.00 0.00 3.07
1099 1110 3.045142 CGGCAATGGGGATGATGC 58.955 61.111 0.00 0.00 38.06 3.91
1101 1112 3.045142 GCAATGGGGATGATGCCG 58.955 61.111 0.00 0.00 32.73 5.69
1102 1113 1.529010 GCAATGGGGATGATGCCGA 60.529 57.895 0.00 0.00 32.73 5.54
1103 1114 0.896940 GCAATGGGGATGATGCCGAT 60.897 55.000 0.00 0.00 32.73 4.18
1212 1247 3.327757 TGCTTGATGAGGACTGGTACTTT 59.672 43.478 0.00 0.00 0.00 2.66
1320 1355 3.950232 GGAGCCGGTCCACAGATA 58.050 61.111 11.91 0.00 46.10 1.98
1656 1697 2.971452 GCTCCTTTCTCCGGTCGT 59.029 61.111 0.00 0.00 0.00 4.34
1698 1739 3.962557 CTGGAGATCTTCCCGCCT 58.037 61.111 0.00 0.00 46.19 5.52
2134 2178 2.743928 CACCACCTCAGCGCCTTC 60.744 66.667 2.29 0.00 0.00 3.46
2172 2216 7.668525 AAGTACACAAGGAAATACTAGTTGC 57.331 36.000 0.00 0.00 0.00 4.17
2184 2228 6.391227 AATACTAGTTGCTGCTTGTGTTTT 57.609 33.333 0.00 0.00 0.00 2.43
2200 2244 6.687081 TGTGTTTTGGTTGAGTAGGTTTAG 57.313 37.500 0.00 0.00 0.00 1.85
2396 2826 8.549338 AGTAACTTTAGTTTAGATTGCCTGAC 57.451 34.615 0.00 0.00 39.31 3.51
2465 2895 5.441718 TTCCATCTTATTGCCAGTCTCTT 57.558 39.130 0.00 0.00 0.00 2.85
2606 3036 2.103941 TGTGTAGAGTTGTGGATGCACA 59.896 45.455 16.89 16.89 33.90 4.57
2770 3208 6.183361 TGGCCATAATCTTGCCTTACTTAGAT 60.183 38.462 0.00 0.00 45.56 1.98
2817 3255 7.592439 AGGACTAAACAACTAGCGTAATTTC 57.408 36.000 0.00 0.00 0.00 2.17
2922 3360 6.486941 ACTATAGCTATCTGTTACTCCCTCC 58.513 44.000 10.16 0.00 0.00 4.30
2923 3361 2.588620 AGCTATCTGTTACTCCCTCCG 58.411 52.381 0.00 0.00 0.00 4.63
2924 3362 2.091775 AGCTATCTGTTACTCCCTCCGT 60.092 50.000 0.00 0.00 0.00 4.69
2925 3363 2.293955 GCTATCTGTTACTCCCTCCGTC 59.706 54.545 0.00 0.00 0.00 4.79
2926 3364 1.777941 ATCTGTTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
2927 3365 0.679002 TCTGTTACTCCCTCCGTCCG 60.679 60.000 0.00 0.00 0.00 4.79
2928 3366 0.679002 CTGTTACTCCCTCCGTCCGA 60.679 60.000 0.00 0.00 0.00 4.55
2929 3367 0.251297 TGTTACTCCCTCCGTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
2930 3368 0.890683 GTTACTCCCTCCGTCCGAAA 59.109 55.000 0.00 0.00 0.00 3.46
2931 3369 1.273327 GTTACTCCCTCCGTCCGAAAA 59.727 52.381 0.00 0.00 0.00 2.29
2932 3370 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2933 3371 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2934 3372 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2935 3373 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2936 3374 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2937 3375 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2938 3376 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2939 3377 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2940 3378 2.928116 CTCCGTCCGAAAATACTTGTCC 59.072 50.000 0.00 0.00 0.00 4.02
2941 3379 2.564062 TCCGTCCGAAAATACTTGTCCT 59.436 45.455 0.00 0.00 0.00 3.85
2942 3380 3.763360 TCCGTCCGAAAATACTTGTCCTA 59.237 43.478 0.00 0.00 0.00 2.94
2943 3381 3.861689 CCGTCCGAAAATACTTGTCCTAC 59.138 47.826 0.00 0.00 0.00 3.18
2944 3382 4.487948 CGTCCGAAAATACTTGTCCTACA 58.512 43.478 0.00 0.00 0.00 2.74
2945 3383 4.561606 CGTCCGAAAATACTTGTCCTACAG 59.438 45.833 0.00 0.00 0.00 2.74
2946 3384 5.620654 CGTCCGAAAATACTTGTCCTACAGA 60.621 44.000 0.00 0.00 0.00 3.41
2947 3385 6.338937 GTCCGAAAATACTTGTCCTACAGAT 58.661 40.000 0.00 0.00 0.00 2.90
2948 3386 6.255887 GTCCGAAAATACTTGTCCTACAGATG 59.744 42.308 0.00 0.00 0.00 2.90
2949 3387 6.153851 TCCGAAAATACTTGTCCTACAGATGA 59.846 38.462 0.00 0.00 0.00 2.92
2950 3388 6.816640 CCGAAAATACTTGTCCTACAGATGAA 59.183 38.462 0.00 0.00 0.00 2.57
2951 3389 7.495934 CCGAAAATACTTGTCCTACAGATGAAT 59.504 37.037 0.00 0.00 0.00 2.57
2952 3390 9.529325 CGAAAATACTTGTCCTACAGATGAATA 57.471 33.333 0.00 0.00 0.00 1.75
2959 3397 9.739276 ACTTGTCCTACAGATGAATAAAATGAA 57.261 29.630 0.00 0.00 0.00 2.57
2962 3400 9.685276 TGTCCTACAGATGAATAAAATGAATGT 57.315 29.630 0.00 0.00 0.00 2.71
3004 3442 8.644374 AGTCTAGATACATCCATTTCTAGGAC 57.356 38.462 0.00 0.00 38.67 3.85
3005 3443 8.228206 AGTCTAGATACATCCATTTCTAGGACA 58.772 37.037 0.00 0.00 38.67 4.02
3006 3444 8.861086 GTCTAGATACATCCATTTCTAGGACAA 58.139 37.037 0.00 0.00 38.67 3.18
3007 3445 9.083422 TCTAGATACATCCATTTCTAGGACAAG 57.917 37.037 6.10 0.00 38.67 3.16
3008 3446 7.682787 AGATACATCCATTTCTAGGACAAGT 57.317 36.000 0.00 0.00 38.13 3.16
3009 3447 8.783660 AGATACATCCATTTCTAGGACAAGTA 57.216 34.615 0.00 0.00 38.13 2.24
3010 3448 9.386122 AGATACATCCATTTCTAGGACAAGTAT 57.614 33.333 0.00 0.00 38.13 2.12
3013 3451 8.738645 ACATCCATTTCTAGGACAAGTATTTC 57.261 34.615 0.00 0.00 38.13 2.17
3014 3452 7.775561 ACATCCATTTCTAGGACAAGTATTTCC 59.224 37.037 0.00 0.00 38.13 3.13
3015 3453 7.265599 TCCATTTCTAGGACAAGTATTTCCA 57.734 36.000 0.00 0.00 33.92 3.53
3016 3454 7.338710 TCCATTTCTAGGACAAGTATTTCCAG 58.661 38.462 0.00 0.00 33.92 3.86
3017 3455 7.182026 TCCATTTCTAGGACAAGTATTTCCAGA 59.818 37.037 0.00 0.00 33.92 3.86
3018 3456 7.281100 CCATTTCTAGGACAAGTATTTCCAGAC 59.719 40.741 0.00 0.00 33.92 3.51
3019 3457 5.578005 TCTAGGACAAGTATTTCCAGACG 57.422 43.478 0.00 0.00 33.92 4.18
3020 3458 3.611766 AGGACAAGTATTTCCAGACGG 57.388 47.619 0.00 0.00 33.92 4.79
3021 3459 3.170717 AGGACAAGTATTTCCAGACGGA 58.829 45.455 0.00 0.00 40.60 4.69
3022 3460 3.195825 AGGACAAGTATTTCCAGACGGAG 59.804 47.826 0.00 0.00 44.10 4.63
3023 3461 3.522553 GACAAGTATTTCCAGACGGAGG 58.477 50.000 0.00 0.00 44.10 4.30
3024 3462 2.236395 ACAAGTATTTCCAGACGGAGGG 59.764 50.000 0.00 0.00 44.10 4.30
3174 3634 9.440784 TGTTCAAAAGACGTCAATTACAATAAC 57.559 29.630 19.50 10.01 0.00 1.89
3209 3676 7.858715 ATTATCCCCTATACTCCTACTGGTA 57.141 40.000 0.00 0.00 34.23 3.25
3275 3742 0.684535 AAGAAATGCCCGGGTTTTGG 59.315 50.000 24.63 0.00 0.00 3.28
3346 3816 2.637382 TCACCTTGAGCATGAGTGGTAA 59.363 45.455 0.00 0.00 35.91 2.85
3489 4004 2.822561 TCAGAATGAGCTTGAGTCGTCT 59.177 45.455 0.00 0.00 42.56 4.18
3936 4452 2.544267 GTCGTCACCTTTCCAGAAACAG 59.456 50.000 0.00 0.00 0.00 3.16
4192 4721 3.426615 ACCTCACCTTGAGTAGTCTGAG 58.573 50.000 7.32 7.32 42.80 3.35
4343 4874 4.183539 GTCTGAACGAGACTTGTGTTTG 57.816 45.455 0.00 0.00 46.85 2.93
4344 4875 3.001330 GTCTGAACGAGACTTGTGTTTGG 59.999 47.826 0.00 0.00 46.85 3.28
4359 4890 4.096532 TGTGTTTGGTCATTGAAGCGTAAA 59.903 37.500 0.00 0.00 0.00 2.01
4372 4903 8.788813 CATTGAAGCGTAAAACATTGTTAGATC 58.211 33.333 1.76 0.00 0.00 2.75
4377 4908 7.464358 AGCGTAAAACATTGTTAGATCATGTC 58.536 34.615 1.76 0.00 0.00 3.06
4415 4946 1.725931 GCGATGTTTTTCTGGCGTCTG 60.726 52.381 0.00 0.00 0.00 3.51
4424 4955 1.523711 CTGGCGTCTGTGTGGTTGT 60.524 57.895 0.00 0.00 0.00 3.32
4567 5110 2.673523 CTGGCACTAGCAGGGCTT 59.326 61.111 9.72 0.00 45.92 4.35
4722 5278 1.334960 GGACGTGAAATGCACTGTTGG 60.335 52.381 0.00 0.00 45.49 3.77
4864 5421 0.107410 TTGTTCCTTGTCACGCTGGT 60.107 50.000 0.00 0.00 0.00 4.00
4885 5442 0.036388 TGGCTCCAACGAAGATGACC 60.036 55.000 0.00 0.00 29.10 4.02
4920 5477 5.244178 CCAACACTACTCAAGACTAGAACCT 59.756 44.000 0.00 0.00 0.00 3.50
4927 5484 6.248569 ACTCAAGACTAGAACCTTCCAAAA 57.751 37.500 0.00 0.00 0.00 2.44
4932 5489 5.155905 AGACTAGAACCTTCCAAAAGAGGA 58.844 41.667 0.00 0.00 34.14 3.71
4936 5503 0.400594 ACCTTCCAAAAGAGGACCCG 59.599 55.000 0.00 0.00 37.42 5.28
5077 5645 0.940126 GCAGATATTGAGCACCCGTG 59.060 55.000 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.679505 TGCTAGCGTGAACCACTTCT 59.320 50.000 10.77 0.00 31.34 2.85
1 2 1.394917 CATGCTAGCGTGAACCACTTC 59.605 52.381 29.43 0.00 35.09 3.01
2 3 1.001974 TCATGCTAGCGTGAACCACTT 59.998 47.619 32.41 0.00 38.81 3.16
3 4 0.608130 TCATGCTAGCGTGAACCACT 59.392 50.000 32.41 0.00 38.81 4.00
4 5 1.328680 CATCATGCTAGCGTGAACCAC 59.671 52.381 36.33 0.00 44.00 4.16
5 6 1.206849 TCATCATGCTAGCGTGAACCA 59.793 47.619 36.33 22.71 44.00 3.67
6 7 1.939974 TCATCATGCTAGCGTGAACC 58.060 50.000 36.33 0.00 44.00 3.62
7 8 2.222678 CCATCATCATGCTAGCGTGAAC 59.777 50.000 36.33 0.00 44.00 3.18
8 9 2.486918 CCATCATCATGCTAGCGTGAA 58.513 47.619 36.33 24.64 44.00 3.18
9 10 1.270465 CCCATCATCATGCTAGCGTGA 60.270 52.381 35.24 35.24 44.76 4.35
10 11 1.154197 CCCATCATCATGCTAGCGTG 58.846 55.000 27.80 27.80 0.00 5.34
11 12 0.035881 CCCCATCATCATGCTAGCGT 59.964 55.000 10.77 6.99 0.00 5.07
12 13 0.675837 CCCCCATCATCATGCTAGCG 60.676 60.000 10.77 0.00 0.00 4.26
13 14 0.403271 ACCCCCATCATCATGCTAGC 59.597 55.000 8.10 8.10 0.00 3.42
26 27 2.135189 CCTTCATAATCTCCACCCCCA 58.865 52.381 0.00 0.00 0.00 4.96
33 34 5.815233 TGAGATCCACCTTCATAATCTCC 57.185 43.478 7.89 0.00 40.95 3.71
39 40 3.118775 CCGTGTTGAGATCCACCTTCATA 60.119 47.826 0.00 0.00 0.00 2.15
60 61 0.680061 ACCTCTTCCTTGACGACACC 59.320 55.000 0.00 0.00 0.00 4.16
67 68 2.028112 CGAACCATGACCTCTTCCTTGA 60.028 50.000 0.00 0.00 0.00 3.02
72 73 3.193691 TCTTCTCGAACCATGACCTCTTC 59.806 47.826 0.00 0.00 0.00 2.87
79 80 2.419159 CCTGCATCTTCTCGAACCATGA 60.419 50.000 0.00 0.00 0.00 3.07
81 82 1.745141 GCCTGCATCTTCTCGAACCAT 60.745 52.381 0.00 0.00 0.00 3.55
101 102 0.716108 GTCGAACTTGAGCATGTCGG 59.284 55.000 0.00 0.00 0.00 4.79
108 109 2.430244 TCGCCGTCGAACTTGAGC 60.430 61.111 0.00 0.00 42.44 4.26
122 123 1.068264 TCGCCATCATAGATCACTCGC 60.068 52.381 0.00 0.00 0.00 5.03
136 137 2.024176 AAAACGATAGCACTCGCCAT 57.976 45.000 7.73 0.00 42.35 4.40
137 138 1.730064 GAAAAACGATAGCACTCGCCA 59.270 47.619 7.73 0.00 42.35 5.69
138 139 1.266891 CGAAAAACGATAGCACTCGCC 60.267 52.381 7.73 0.00 45.77 5.54
141 142 4.506217 GCATACGAAAAACGATAGCACTC 58.494 43.478 0.00 0.00 45.77 3.51
144 145 3.936902 GGCATACGAAAAACGATAGCA 57.063 42.857 0.00 0.00 45.77 3.49
157 158 1.324435 CATCACACTTGTCGGCATACG 59.676 52.381 0.00 0.00 46.11 3.06
166 167 1.202915 TGGTCATGCCATCACACTTGT 60.203 47.619 4.93 0.00 43.61 3.16
194 195 1.643832 GGAGTTTGATCGCGCCATC 59.356 57.895 8.17 8.17 0.00 3.51
201 202 1.521681 GAGGGCGGGAGTTTGATCG 60.522 63.158 0.00 0.00 0.00 3.69
203 204 0.698818 AAAGAGGGCGGGAGTTTGAT 59.301 50.000 0.00 0.00 0.00 2.57
206 207 1.328279 CAAAAAGAGGGCGGGAGTTT 58.672 50.000 0.00 0.00 0.00 2.66
219 220 1.862201 CACATGCCAGCACACAAAAAG 59.138 47.619 0.00 0.00 0.00 2.27
232 233 3.788766 GCGACCGACACACATGCC 61.789 66.667 0.00 0.00 0.00 4.40
291 293 1.265635 GCAGCCAACATACAACGTCAA 59.734 47.619 0.00 0.00 0.00 3.18
294 296 0.874390 CAGCAGCCAACATACAACGT 59.126 50.000 0.00 0.00 0.00 3.99
296 298 0.109132 GCCAGCAGCCAACATACAAC 60.109 55.000 0.00 0.00 34.35 3.32
299 301 0.101759 CATGCCAGCAGCCAACATAC 59.898 55.000 0.00 0.00 42.71 2.39
304 306 2.992689 CACCATGCCAGCAGCCAA 60.993 61.111 0.00 0.00 42.71 4.52
318 320 1.080569 CAAAGTTCATGCCGGCACC 60.081 57.895 35.50 19.83 0.00 5.01
323 326 2.179018 CGCCCAAAGTTCATGCCG 59.821 61.111 0.00 0.00 0.00 5.69
324 327 1.212751 GTCGCCCAAAGTTCATGCC 59.787 57.895 0.00 0.00 0.00 4.40
355 358 1.302752 TGCGGCCATAGATCATGCC 60.303 57.895 2.24 0.00 32.84 4.40
370 373 2.871633 ACAAATTTGAAAAAGGCCTGCG 59.128 40.909 24.64 0.00 0.00 5.18
371 374 3.548616 GCACAAATTTGAAAAAGGCCTGC 60.549 43.478 24.64 15.47 0.00 4.85
373 376 3.883669 TGCACAAATTTGAAAAAGGCCT 58.116 36.364 24.64 0.00 0.00 5.19
393 396 3.124128 CCGCGACTCATTTCATATCCATG 59.876 47.826 8.23 0.00 0.00 3.66
394 397 3.329386 CCGCGACTCATTTCATATCCAT 58.671 45.455 8.23 0.00 0.00 3.41
395 398 2.547855 CCCGCGACTCATTTCATATCCA 60.548 50.000 8.23 0.00 0.00 3.41
397 400 2.476619 CACCCGCGACTCATTTCATATC 59.523 50.000 8.23 0.00 0.00 1.63
399 402 1.206132 ACACCCGCGACTCATTTCATA 59.794 47.619 8.23 0.00 0.00 2.15
417 420 1.169661 GGTCGGCAATGTGTCCAACA 61.170 55.000 0.00 0.00 44.79 3.33
423 426 0.887933 GATTTGGGTCGGCAATGTGT 59.112 50.000 0.00 0.00 0.00 3.72
425 428 1.923356 AAGATTTGGGTCGGCAATGT 58.077 45.000 0.00 0.00 0.00 2.71
428 431 3.223435 TGTTTAAGATTTGGGTCGGCAA 58.777 40.909 0.00 0.00 0.00 4.52
466 469 3.192922 CCGTTTGGATCGGCCGTC 61.193 66.667 27.15 20.82 41.48 4.79
467 470 3.697747 TCCGTTTGGATCGGCCGT 61.698 61.111 27.15 12.96 46.49 5.68
475 478 2.683867 ACGATGTTTTTGTCCGTTTGGA 59.316 40.909 0.00 0.00 43.88 3.53
483 486 4.865776 TCCAAATGGACGATGTTTTTGTC 58.134 39.130 0.00 0.00 39.78 3.18
498 501 3.804325 ACTCTAACGCATCGATCCAAATG 59.196 43.478 0.00 0.00 0.00 2.32
505 508 2.099921 AGAGCAACTCTAACGCATCGAT 59.900 45.455 0.00 0.00 39.28 3.59
509 512 9.197694 CTTTATATAAGAGCAACTCTAACGCAT 57.802 33.333 0.00 0.00 40.28 4.73
510 513 7.652105 CCTTTATATAAGAGCAACTCTAACGCA 59.348 37.037 0.00 0.00 40.28 5.24
516 519 8.982723 TCTGTTCCTTTATATAAGAGCAACTCT 58.017 33.333 10.30 0.00 43.37 3.24
534 537 9.700831 AGGCAAATATATACTTTTTCTGTTCCT 57.299 29.630 0.00 0.00 0.00 3.36
538 541 9.391006 TCGAAGGCAAATATATACTTTTTCTGT 57.609 29.630 0.00 0.00 0.00 3.41
539 542 9.869844 CTCGAAGGCAAATATATACTTTTTCTG 57.130 33.333 0.00 0.00 0.00 3.02
540 543 9.057089 CCTCGAAGGCAAATATATACTTTTTCT 57.943 33.333 0.00 0.00 0.00 2.52
541 544 9.052759 TCCTCGAAGGCAAATATATACTTTTTC 57.947 33.333 0.00 0.00 34.61 2.29
542 545 8.974060 TCCTCGAAGGCAAATATATACTTTTT 57.026 30.769 0.00 0.00 34.61 1.94
543 546 9.220767 GATCCTCGAAGGCAAATATATACTTTT 57.779 33.333 0.00 0.00 34.61 2.27
544 547 8.375506 TGATCCTCGAAGGCAAATATATACTTT 58.624 33.333 0.00 0.00 34.61 2.66
545 548 7.907389 TGATCCTCGAAGGCAAATATATACTT 58.093 34.615 0.00 0.00 34.61 2.24
546 549 7.482169 TGATCCTCGAAGGCAAATATATACT 57.518 36.000 0.00 0.00 34.61 2.12
547 550 8.723942 ATTGATCCTCGAAGGCAAATATATAC 57.276 34.615 0.00 0.00 34.61 1.47
549 552 9.911788 ATTATTGATCCTCGAAGGCAAATATAT 57.088 29.630 0.00 0.00 34.61 0.86
551 554 9.167311 GTATTATTGATCCTCGAAGGCAAATAT 57.833 33.333 0.00 0.00 34.61 1.28
552 555 8.154203 TGTATTATTGATCCTCGAAGGCAAATA 58.846 33.333 0.00 0.00 34.61 1.40
553 556 6.998074 TGTATTATTGATCCTCGAAGGCAAAT 59.002 34.615 0.00 0.00 34.61 2.32
554 557 6.353323 TGTATTATTGATCCTCGAAGGCAAA 58.647 36.000 0.00 0.00 34.61 3.68
555 558 5.924356 TGTATTATTGATCCTCGAAGGCAA 58.076 37.500 0.00 0.00 34.61 4.52
556 559 5.545063 TGTATTATTGATCCTCGAAGGCA 57.455 39.130 0.00 0.00 34.61 4.75
557 560 5.582665 GGATGTATTATTGATCCTCGAAGGC 59.417 44.000 0.00 0.00 34.61 4.35
558 561 6.591834 GTGGATGTATTATTGATCCTCGAAGG 59.408 42.308 0.00 0.00 37.20 3.46
559 562 6.591834 GGTGGATGTATTATTGATCCTCGAAG 59.408 42.308 0.00 0.00 37.20 3.79
560 563 6.270000 AGGTGGATGTATTATTGATCCTCGAA 59.730 38.462 0.00 0.00 37.20 3.71
561 564 5.780282 AGGTGGATGTATTATTGATCCTCGA 59.220 40.000 0.00 0.00 37.20 4.04
562 565 6.042638 AGGTGGATGTATTATTGATCCTCG 57.957 41.667 0.00 0.00 37.20 4.63
563 566 7.009179 TGAGGTGGATGTATTATTGATCCTC 57.991 40.000 0.00 0.00 37.20 3.71
564 567 7.579940 ATGAGGTGGATGTATTATTGATCCT 57.420 36.000 0.00 0.00 37.20 3.24
565 568 9.388506 CTAATGAGGTGGATGTATTATTGATCC 57.611 37.037 0.00 0.00 36.87 3.36
566 569 8.887717 GCTAATGAGGTGGATGTATTATTGATC 58.112 37.037 0.00 0.00 0.00 2.92
567 570 7.831193 GGCTAATGAGGTGGATGTATTATTGAT 59.169 37.037 0.00 0.00 0.00 2.57
568 571 7.168219 GGCTAATGAGGTGGATGTATTATTGA 58.832 38.462 0.00 0.00 0.00 2.57
569 572 6.942005 TGGCTAATGAGGTGGATGTATTATTG 59.058 38.462 0.00 0.00 0.00 1.90
583 586 4.703379 AGAGAAGGATTGGCTAATGAGG 57.297 45.455 0.00 0.00 0.00 3.86
585 588 6.560304 AGGAATAGAGAAGGATTGGCTAATGA 59.440 38.462 0.00 0.00 0.00 2.57
601 605 3.158676 CCCCTCCGTAGAAGGAATAGAG 58.841 54.545 0.00 0.00 26.72 2.43
610 614 1.601419 CGTCAAGCCCCTCCGTAGAA 61.601 60.000 0.00 0.00 0.00 2.10
611 615 2.050350 CGTCAAGCCCCTCCGTAGA 61.050 63.158 0.00 0.00 0.00 2.59
612 616 2.494918 CGTCAAGCCCCTCCGTAG 59.505 66.667 0.00 0.00 0.00 3.51
613 617 3.072468 CCGTCAAGCCCCTCCGTA 61.072 66.667 0.00 0.00 0.00 4.02
615 619 4.016706 AACCGTCAAGCCCCTCCG 62.017 66.667 0.00 0.00 0.00 4.63
616 620 2.359975 CAACCGTCAAGCCCCTCC 60.360 66.667 0.00 0.00 0.00 4.30
617 621 2.359975 CCAACCGTCAAGCCCCTC 60.360 66.667 0.00 0.00 0.00 4.30
618 622 4.660938 GCCAACCGTCAAGCCCCT 62.661 66.667 0.00 0.00 0.00 4.79
631 635 0.312416 AACAAAAGCATACGCGCCAA 59.688 45.000 5.73 0.00 45.49 4.52
634 638 1.720330 GCGAACAAAAGCATACGCGC 61.720 55.000 5.73 0.00 45.49 6.86
635 639 2.256247 GCGAACAAAAGCATACGCG 58.744 52.632 3.53 3.53 45.49 6.01
643 647 1.028905 TCCAACCCAGCGAACAAAAG 58.971 50.000 0.00 0.00 0.00 2.27
662 666 1.374252 GATCGTTCGCACTGGGTGT 60.374 57.895 0.00 0.00 35.75 4.16
689 693 1.921346 TCGGCTCCCTGGGCTTTTA 60.921 57.895 8.22 0.00 0.00 1.52
695 699 4.452733 GAACGTCGGCTCCCTGGG 62.453 72.222 6.33 6.33 0.00 4.45
696 700 4.452733 GGAACGTCGGCTCCCTGG 62.453 72.222 0.00 0.00 0.00 4.45
775 779 5.184340 AGAGAGATACGTCAAATTACCGG 57.816 43.478 0.00 0.00 0.00 5.28
861 866 2.366533 CGCAGGGAGTCTCAGTTACTA 58.633 52.381 1.47 0.00 0.00 1.82
863 868 0.458716 GCGCAGGGAGTCTCAGTTAC 60.459 60.000 0.30 0.00 0.00 2.50
1086 1097 0.773014 TCATCGGCATCATCCCCATT 59.227 50.000 0.00 0.00 0.00 3.16
1087 1098 0.997363 ATCATCGGCATCATCCCCAT 59.003 50.000 0.00 0.00 0.00 4.00
1088 1099 0.037160 CATCATCGGCATCATCCCCA 59.963 55.000 0.00 0.00 0.00 4.96
1089 1100 0.679002 CCATCATCGGCATCATCCCC 60.679 60.000 0.00 0.00 0.00 4.81
1090 1101 0.679002 CCCATCATCGGCATCATCCC 60.679 60.000 0.00 0.00 0.00 3.85
1091 1102 0.679002 CCCCATCATCGGCATCATCC 60.679 60.000 0.00 0.00 0.00 3.51
1092 1103 1.310933 GCCCCATCATCGGCATCATC 61.311 60.000 0.00 0.00 45.01 2.92
1093 1104 1.303888 GCCCCATCATCGGCATCAT 60.304 57.895 0.00 0.00 45.01 2.45
1094 1105 2.113774 GCCCCATCATCGGCATCA 59.886 61.111 0.00 0.00 45.01 3.07
1098 1109 3.839353 CTCCTGCCCCATCATCGGC 62.839 68.421 0.00 0.00 45.92 5.54
1099 1110 2.429058 CTCCTGCCCCATCATCGG 59.571 66.667 0.00 0.00 0.00 4.18
1100 1111 2.429058 CCTCCTGCCCCATCATCG 59.571 66.667 0.00 0.00 0.00 3.84
1101 1112 2.114838 GCCTCCTGCCCCATCATC 59.885 66.667 0.00 0.00 0.00 2.92
1102 1113 2.369291 AGCCTCCTGCCCCATCAT 60.369 61.111 0.00 0.00 42.71 2.45
1103 1114 3.414193 CAGCCTCCTGCCCCATCA 61.414 66.667 0.00 0.00 42.71 3.07
1266 1301 2.517875 GATGCTTCCATGGCGGCT 60.518 61.111 22.72 12.56 33.14 5.52
1320 1355 1.604378 CAGGTTGAGGAGCGGGAAT 59.396 57.895 0.00 0.00 0.00 3.01
1404 1445 2.548295 GCCAAGGAACGCCGTGAAA 61.548 57.895 0.00 0.00 45.22 2.69
1629 1670 1.002087 GAGAAAGGAGCGGTCAAGGAA 59.998 52.381 17.59 0.00 0.00 3.36
2134 2178 3.802139 TGTGTACTTTGCGAAACTCTGAG 59.198 43.478 2.45 2.45 0.00 3.35
2172 2216 3.508744 ACTCAACCAAAACACAAGCAG 57.491 42.857 0.00 0.00 0.00 4.24
2184 2228 4.650972 ATTGCCTAAACCTACTCAACCA 57.349 40.909 0.00 0.00 0.00 3.67
2218 2646 7.199766 AGTGCACAAAATTCGTCAAGATTAAA 58.800 30.769 21.04 0.00 0.00 1.52
2465 2895 1.348696 TGAACATGAGGCAGCAGAGAA 59.651 47.619 0.00 0.00 0.00 2.87
2541 2971 6.291060 GCGCAATAACTGACCGATTTTTATTG 60.291 38.462 0.30 7.65 40.64 1.90
2606 3036 6.533730 TCTATGACACATTCTTGAAACTGGT 58.466 36.000 0.00 0.00 0.00 4.00
2649 3087 2.958818 AGACAGACCAAGGAGTGTGTA 58.041 47.619 0.00 0.00 43.63 2.90
2805 3243 8.651588 CAATAGCTAGGAATGAAATTACGCTAG 58.348 37.037 0.00 0.00 43.80 3.42
2911 3349 0.890683 TTTCGGACGGAGGGAGTAAC 59.109 55.000 0.00 0.00 0.00 2.50
2914 3352 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
2915 3353 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2916 3354 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2917 3355 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2918 3356 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2919 3357 2.928116 GGACAAGTATTTTCGGACGGAG 59.072 50.000 0.00 0.00 0.00 4.63
2920 3358 2.564062 AGGACAAGTATTTTCGGACGGA 59.436 45.455 0.00 0.00 0.00 4.69
2921 3359 2.968675 AGGACAAGTATTTTCGGACGG 58.031 47.619 0.00 0.00 0.00 4.79
2922 3360 4.487948 TGTAGGACAAGTATTTTCGGACG 58.512 43.478 0.00 0.00 0.00 4.79
2923 3361 5.717119 TCTGTAGGACAAGTATTTTCGGAC 58.283 41.667 0.00 0.00 0.00 4.79
2924 3362 5.988310 TCTGTAGGACAAGTATTTTCGGA 57.012 39.130 0.00 0.00 0.00 4.55
2925 3363 6.338146 TCATCTGTAGGACAAGTATTTTCGG 58.662 40.000 0.00 0.00 0.00 4.30
2926 3364 7.827819 TTCATCTGTAGGACAAGTATTTTCG 57.172 36.000 0.00 0.00 0.00 3.46
2933 3371 9.739276 TTCATTTTATTCATCTGTAGGACAAGT 57.261 29.630 0.00 0.00 0.00 3.16
2936 3374 9.685276 ACATTCATTTTATTCATCTGTAGGACA 57.315 29.630 0.00 0.00 0.00 4.02
2978 3416 9.084533 GTCCTAGAAATGGATGTATCTAGACTT 57.915 37.037 9.60 0.00 42.48 3.01
2979 3417 8.228206 TGTCCTAGAAATGGATGTATCTAGACT 58.772 37.037 9.60 0.00 42.48 3.24
2980 3418 8.410673 TGTCCTAGAAATGGATGTATCTAGAC 57.589 38.462 9.60 7.06 42.48 2.59
2981 3419 9.083422 CTTGTCCTAGAAATGGATGTATCTAGA 57.917 37.037 9.60 0.00 42.48 2.43
2982 3420 8.865090 ACTTGTCCTAGAAATGGATGTATCTAG 58.135 37.037 0.00 0.00 40.55 2.43
2983 3421 8.783660 ACTTGTCCTAGAAATGGATGTATCTA 57.216 34.615 0.00 0.00 35.87 1.98
2984 3422 7.682787 ACTTGTCCTAGAAATGGATGTATCT 57.317 36.000 0.00 0.00 35.87 1.98
2987 3425 9.832445 GAAATACTTGTCCTAGAAATGGATGTA 57.168 33.333 0.00 0.00 35.87 2.29
2988 3426 7.775561 GGAAATACTTGTCCTAGAAATGGATGT 59.224 37.037 0.00 0.00 35.87 3.06
2989 3427 7.775093 TGGAAATACTTGTCCTAGAAATGGATG 59.225 37.037 0.00 0.00 35.87 3.51
2990 3428 7.872138 TGGAAATACTTGTCCTAGAAATGGAT 58.128 34.615 0.00 0.00 35.87 3.41
2991 3429 7.182026 TCTGGAAATACTTGTCCTAGAAATGGA 59.818 37.037 0.00 0.00 34.77 3.41
2992 3430 7.281100 GTCTGGAAATACTTGTCCTAGAAATGG 59.719 40.741 0.00 0.00 34.77 3.16
2993 3431 7.010552 CGTCTGGAAATACTTGTCCTAGAAATG 59.989 40.741 0.00 0.00 34.77 2.32
2994 3432 7.042335 CGTCTGGAAATACTTGTCCTAGAAAT 58.958 38.462 0.00 0.00 34.77 2.17
2995 3433 6.395629 CGTCTGGAAATACTTGTCCTAGAAA 58.604 40.000 0.00 0.00 34.77 2.52
2996 3434 5.105473 CCGTCTGGAAATACTTGTCCTAGAA 60.105 44.000 0.00 0.00 37.49 2.10
2997 3435 4.401519 CCGTCTGGAAATACTTGTCCTAGA 59.598 45.833 0.00 0.00 37.49 2.43
2998 3436 4.401519 TCCGTCTGGAAATACTTGTCCTAG 59.598 45.833 0.00 0.00 42.85 3.02
2999 3437 4.346730 TCCGTCTGGAAATACTTGTCCTA 58.653 43.478 0.00 0.00 42.85 2.94
3000 3438 3.170717 TCCGTCTGGAAATACTTGTCCT 58.829 45.455 0.00 0.00 42.85 3.85
3001 3439 3.522553 CTCCGTCTGGAAATACTTGTCC 58.477 50.000 0.00 0.00 45.87 4.02
3002 3440 3.522553 CCTCCGTCTGGAAATACTTGTC 58.477 50.000 0.00 0.00 45.87 3.18
3003 3441 2.236395 CCCTCCGTCTGGAAATACTTGT 59.764 50.000 0.00 0.00 45.87 3.16
3004 3442 2.500098 TCCCTCCGTCTGGAAATACTTG 59.500 50.000 0.00 0.00 45.87 3.16
3005 3443 2.766828 CTCCCTCCGTCTGGAAATACTT 59.233 50.000 0.00 0.00 45.87 2.24
3006 3444 2.292323 ACTCCCTCCGTCTGGAAATACT 60.292 50.000 0.00 0.00 45.87 2.12
3007 3445 2.108970 ACTCCCTCCGTCTGGAAATAC 58.891 52.381 0.00 0.00 45.87 1.89
3008 3446 2.544844 ACTCCCTCCGTCTGGAAATA 57.455 50.000 0.00 0.00 45.87 1.40
3009 3447 2.108970 GTACTCCCTCCGTCTGGAAAT 58.891 52.381 0.00 0.00 45.87 2.17
3010 3448 1.076677 AGTACTCCCTCCGTCTGGAAA 59.923 52.381 0.00 0.00 45.87 3.13
3011 3449 0.702902 AGTACTCCCTCCGTCTGGAA 59.297 55.000 0.00 0.00 45.87 3.53
3012 3450 1.211457 GTAGTACTCCCTCCGTCTGGA 59.789 57.143 0.00 0.00 43.88 3.86
3013 3451 1.212441 AGTAGTACTCCCTCCGTCTGG 59.788 57.143 0.00 0.00 0.00 3.86
3014 3452 2.290464 CAGTAGTACTCCCTCCGTCTG 58.710 57.143 0.00 0.00 0.00 3.51
3015 3453 1.914798 ACAGTAGTACTCCCTCCGTCT 59.085 52.381 0.00 0.00 0.00 4.18
3016 3454 2.416680 ACAGTAGTACTCCCTCCGTC 57.583 55.000 0.00 0.00 0.00 4.79
3017 3455 5.839517 ATATACAGTAGTACTCCCTCCGT 57.160 43.478 0.00 0.00 31.96 4.69
3018 3456 8.804912 AATAATATACAGTAGTACTCCCTCCG 57.195 38.462 0.00 0.00 31.96 4.63
3019 3457 9.750783 TGAATAATATACAGTAGTACTCCCTCC 57.249 37.037 0.00 0.00 31.96 4.30
3021 3459 9.756571 CCTGAATAATATACAGTAGTACTCCCT 57.243 37.037 0.00 0.00 31.96 4.20
3022 3460 9.531158 ACCTGAATAATATACAGTAGTACTCCC 57.469 37.037 0.00 0.00 31.96 4.30
3090 3550 1.393196 GCATTTTTATGGCCGTGCAAC 59.607 47.619 8.05 0.00 33.09 4.17
3123 3583 1.067212 CACGATGTACAGTAGCCTCCC 59.933 57.143 0.33 0.00 0.00 4.30
3253 3720 3.210227 CAAAACCCGGGCATTTCTTTTT 58.790 40.909 24.08 15.13 0.00 1.94
3258 3725 0.246360 CTCCAAAACCCGGGCATTTC 59.754 55.000 24.08 0.00 0.00 2.17
3297 3767 8.287439 TCTGTTCAGAAAAAGAACCATAACAA 57.713 30.769 0.00 0.00 43.57 2.83
3346 3816 6.782082 TCACTAGACTATGCAGACAAGAAT 57.218 37.500 0.00 0.00 0.00 2.40
3483 3998 1.153349 GGGCATGGAAGGAGACGAC 60.153 63.158 0.00 0.00 0.00 4.34
3486 4001 1.144936 CGAGGGCATGGAAGGAGAC 59.855 63.158 0.00 0.00 0.00 3.36
3489 4004 2.688666 AGCGAGGGCATGGAAGGA 60.689 61.111 0.00 0.00 43.41 3.36
3561 4076 2.363795 TCCTCCTTCACGCGGGAT 60.364 61.111 14.07 0.00 0.00 3.85
3936 4452 7.620394 GCAAGATAAGTCGAGTTTTCTCTTCAC 60.620 40.741 21.42 12.79 44.16 3.18
4098 4625 0.987294 AGCACTATCCTGCACTTGGT 59.013 50.000 0.00 0.00 39.86 3.67
4162 4691 3.096092 CTCAAGGTGAGGTAGCTTCTCT 58.904 50.000 14.98 1.47 44.89 3.10
4192 4721 5.358160 CAGATAAATTGGTTCTGGGAAGGTC 59.642 44.000 5.17 0.00 34.55 3.85
4324 4855 2.936498 ACCAAACACAAGTCTCGTTCAG 59.064 45.455 0.00 0.00 0.00 3.02
4341 4872 4.902443 TGTTTTACGCTTCAATGACCAA 57.098 36.364 0.00 0.00 0.00 3.67
4342 4873 5.218885 CAATGTTTTACGCTTCAATGACCA 58.781 37.500 0.00 0.00 0.00 4.02
4343 4874 5.219633 ACAATGTTTTACGCTTCAATGACC 58.780 37.500 0.00 0.00 0.00 4.02
4344 4875 6.747659 AACAATGTTTTACGCTTCAATGAC 57.252 33.333 0.00 0.00 0.00 3.06
4359 4890 8.446273 CGAAAAGAGACATGATCTAACAATGTT 58.554 33.333 3.43 3.43 38.00 2.71
4372 4903 3.365364 GCAAGGAACCGAAAAGAGACATG 60.365 47.826 0.00 0.00 0.00 3.21
4377 4908 0.110192 GCGCAAGGAACCGAAAAGAG 60.110 55.000 0.30 0.00 38.28 2.85
4415 4946 0.179113 CCAAGCCACAACAACCACAC 60.179 55.000 0.00 0.00 0.00 3.82
4424 4955 2.744494 GCAAACCAAATCCAAGCCACAA 60.744 45.455 0.00 0.00 0.00 3.33
4722 5278 3.251974 GCTCTGCAGCAGTGACAC 58.748 61.111 25.42 6.72 46.06 3.67
4864 5421 1.066858 GTCATCTTCGTTGGAGCCAGA 60.067 52.381 0.00 0.00 0.00 3.86
4885 5442 1.732259 GTAGTGTTGGATCGGCACTTG 59.268 52.381 16.71 0.00 42.60 3.16
4920 5477 1.074248 GGCGGGTCCTCTTTTGGAA 59.926 57.895 0.00 0.00 37.93 3.53
4927 5484 4.490706 AGTAATTTATAGGCGGGTCCTCT 58.509 43.478 0.00 0.00 43.20 3.69
4932 5489 4.102681 AGCTGAAGTAATTTATAGGCGGGT 59.897 41.667 0.00 0.00 0.00 5.28
4936 5503 6.763610 AGTGTGAGCTGAAGTAATTTATAGGC 59.236 38.462 0.00 0.00 0.00 3.93
4995 5562 4.067896 TGGAACATGAAGAGAGCAGTTTC 58.932 43.478 0.00 0.00 0.00 2.78
5055 5623 1.202568 CGGGTGCTCAATATCTGCTCA 60.203 52.381 0.00 0.00 0.00 4.26


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.